In road bike sizing, you would probably need a 54 or 56cm bike. If in doubt, go with the smaller size. In mountain bike sizing, you would probably need about a 19-20" frame. For commuting you probably want a bike that can easily take a rear rack and that has some fairly decent tire clearance.

If you're 'ok' with buying online Nashbar.com has a pretty big sale going on for Father's Day. Bikesdirect.com is another place you should check out. Note that to buy online you should be at least a little bit experienced with bikes, or otherwise mechanically inclined and willing to learn.

For a commute as short as 3 miles, almost any bike would work without any trouble. By far the most important thing to worry about is that the bike is a good fit for you (as far as sizing).